Naturally Occurring Mutations of SARS-CoV-2 Main Protease Confer Drug Resistance to Nirmatrelvir

ACS Central Science, Год журнала: 2023, Номер 9(8), С. 1658 - 1669

Опубликована: Июль 24, 2023

The SARS-CoV-2 main protease (Mpro) is the drug target of Pfizer's oral nirmatrelvir. emergence variants with mutations in Mpro raised alarm potential resistance. To identify clinically relevant drug-resistant mutants, we systematically characterized 102 naturally occurring mutants located at 12 residues nirmatrelvir-binding site, among which 22 5 residues, including S144M/F/A/G/Y, M165T, E166 V/G/A, H172Q/F, and Q192T/S/L/A/I/P/H/V/W/C/F, showed comparable enzymatic activity to wild-type (kcat/Km < 10-fold change) while being resistant nirmatrelvir (Ki > increase). X-ray crystal structures were determined for six representative and/or without GC-376/nirmatrelvir. Using recombinant viruses generated from reverse genetics, confirmed resistance antiviral assay that reduced had attenuated viral replication. Overall, our study identified several hotspots warrant close monitoring possible clinical evidence resistance, some have already emerged independent passage assays conducted by others.

Язык: Английский

---

Nirmatrelvir-resistant SARS-CoV-2 variants with high fitness in an infectious cell culture system

Science Advances, Год журнала: 2022, Номер 8(51)

Опубликована: Дек. 21, 2022

The oral protease inhibitor nirmatrelvir is of key importance for prevention severe coronavirus disease 2019 (COVID-19). To facilitate resistance monitoring, we studied acute respiratory syndrome 2 (SARS-CoV-2) escape from in cell culture. Resistant variants harbored combinations substitutions the SARS-CoV-2 main (Mpro). Reverse genetics revealed that E166V and L50F + conferred high infectious culture, replicon, Mpro systems. While L50F, E166V, decreased replication activity, had fitness system. Naturally occurring compensated cost promoted viral escape. Molecular dynamics simulations weakened nirmatrelvir-Mpro binding. Polymerase remdesivir monoclonal antibody bebtelovimab retained activity against nirmatrelvir-resistant variants, combination with enhanced treatment efficacy compared to individual compounds. These findings have implications monitoring ensuring treatments emerging sarbecoviruses.

Язык: Английский

---

The Substitutions L50F, E166A, and L167F in SARS-CoV-2 3CLpro Are Selected by a Protease Inhibitor In Vitro and Confer Resistance To Nirmatrelvir

mBio, Год журнала: 2023, Номер 14(1)

Опубликована: Янв. 10, 2023

The SARS-CoV-2 main protease (3CLpro) has an indispensable role in the viral life cycle and is a therapeutic target for treatment of COVID-19. potential 3CLpro-inhibitors to select drug-resistant variants needs be established. Therefore, was passaged vitro presence increasing concentrations ALG-097161, probe compound designed context 3CLpro drug discovery program. We identified combination amino acid substitutions (L50F E166A L167F) that associated with >20× increase 50% effective concentration (EC50) values nirmatrelvir (PF-07321332), PF-00835231, ensitrelvir. While two single (E166A provide low-level resistance inhibitors biochemical assay, triple mutant results highest levels (6× 72×). All are significant loss enzymatic activity, suggesting reduction fitness. Structural biology analysis indicates different reduce number inhibitor/enzyme interactions while binding substrate maintained. These observations will important interpretation development clinical setting. IMPORTANCE Paxlovid first oral antiviral approved infection. Antiviral treatments often viruses. In order guide use novel antivirals, it essential understand risk characterize changes genes proteins. this work, we describe time pathway allows develop against vitro. characteristics may predictive situation. our work management COVID-19 next-generation inhibitors.

Язык: Английский

---

Transmissible SARS-CoV-2 variants with resistance to clinical protease inhibitors

Science Advances, Год журнала: 2023, Номер 9(13)

Опубликована: Март 31, 2023

Vaccines and drugs have helped reduce disease severity blunt the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, ongoing virus transmission, continuous evolution, increasing selective pressures potential to yield viral variants capable resisting these interventions. Here, we investigate susceptibility natural main protease [Mpro; 3C-like (3CLpro)] SARS-CoV-2 inhibitors. Multiple single amino acid changes in Mpro confer resistance nirmatrelvir (the active component Paxlovid). An additional clinical-stage inhibitor, ensitrelvir (Xocova), shows a different mutation profile. Importantly, phylogenetic analyses indicate that several resistant pre-existed introduction into human population are spreading. These results encourage monitoring development inhibitors other antiviral with mechanisms action profiles for combinatorial therapy.

Язык: Английский

---

Global prevalence of SARS-CoV-2 3CL protease mutations associated with nirmatrelvir or ensitrelvir resistance

EBioMedicine, Год журнала: 2023, Номер 91, С. 104559 - 104559

Опубликована: Апрель 14, 2023

Nirmatrelvir-ritonavir (Paxlovid) and ensitrelvir are 3-chymotrypsin-like cysteine protease (3CLpro) inhibitors which have been approved for the treatment of COVID-19 in 2021 2022, respectively. Previous studies identified 3CLpro mutations that associated with reduced susceptibility to these antivirals. The aim current study was estimate global prevalence inhibitor-resistant SARS-CoV-2 strains.We compiled a list nirmatrelvir or resistance based on either viral replication activity assays, determined their among 13.4 million sequences deposited GISAID as December 14, about 1 year after approval nirmatrelvir-ritonavir. We analyzed different time periods, lineages geographical locations.Overall, 0.5% (67,095/13,446,588) contained at least one mutation shown affect inhibitory activity. did not observe any increasing trend widespread clinical use G15S (2070 per million) T21I (1386 were most prevalent mutations, dominant some lineages. E166V S144E, previously by > 100-folds, found <1 sequences.Our data suggest inhibitor is currently rare. However, continuous genotypic phenotypic surveillance would be crucial early detection resistant mutants.Richard Carol Yu, May Tam Mak Mei Yin, Shaw Foundation Hong Kong, Michael Tong, Marina Lee, Government Consultancy Service, Emergency Key Program Guangzhou Laboratory (See acknowledgements full list).

Язык: Английский

---

A new generation Mpro inhibitor with potent activity against SARS-CoV-2 Omicron variants

Signal Transduction and Targeted Therapy, Год журнала: 2023, Номер 8(1)

Опубликована: Март 16, 2023

Abstract Emerging SARS-CoV-2 variants, particularly the Omicron variant and its sublineages, continually threaten global public health. Small molecule antivirals are an effective treatment strategy to fight against virus. However, first-generation either show limited clinical efficacy and/or have some defects in pharmacokinetic (PK) properties. Moreover, with increased use of these drugs across globe, they face great pressure drug resistance. We herein present discovery characterization a new generation antiviral candidate (SY110), which is potent selective inhibitor main protease (M pro ). This compound displayed vitro activity not only predominant sublineage BA.5, but also other highly pathogenic human coronaviruses including SARS-CoV-1 MERS-CoV. In Omicron-infected K18-hACE2 mouse model, oral SY110 significantly lowered viral burdens lung alleviated virus-induced pathology. Importantly, possesses favorable PK properties high exposure bioavailability, outstanding safety profile. Furthermore, exhibited sensitivity several drug-resistance M mutations. Collectively, this investigation provides promising variants SARS-CoV-2.

Язык: Английский

---

Multidrug-resistant mutations to antiviral and antibody therapy in an immunocompromised patient infected with SARS-CoV-2

Med, Год журнала: 2023, Номер 4(11), С. 813 - 824.e4

Опубликована: Сен. 7, 2023

Antiviral and antibody therapies for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are being recommended high-risk patients, but the potential development of multidrug-resistant mutations in immunocompromised patients is unclear.To investigate treatment course cases prolonged viral shedding an patient with SARS-CoV-2 infection, we conducted longitudinal measurements laboratory tests, chest computed tomography (CT) image evaluations, titers, antigen levels nasopharyngeal swabs. Furthermore, performed whole-genome sequencing digital PCR analysis to examine mechanisms drug resistance.We present a case 65-year-old man history malignant lymphoma who was treated multiple antiviral therapies, including sotrovimab, remdesivir, paxlovid (nirmatrelvir/ritonavir), molnupiravir. Initially, decreased after treatments. However, virus rebounded, showed no virologic response. The genome revealed single Omicron subvariant (BA.1.1), which evolved within host during disease progression. viruses had acquired resistance nirmatrelvir (3 chymotrypsin-like protease [3CLpro] E166 A/V), sotrovimab (spike P337L E340K), remdesivir (RNA-dependent RNA polymerase [RdRp] V166L).Our results indicate that survival fitness persist infected subpopulation selection pressure.This study supported by JSPS KAKENHI Early-Career Scientists 18K16292 (Y.H.), Grant-in-Aid Scientific Research (B) 20H03668 23H02955 YASUDA Medical Foundation Uehara Memorial Takeda Science Kato Bioscience (Y.H.).

Язык: Английский

---

Olgotrelvir, a dual inhibitor of SARS-CoV-2 Mpro and cathepsin L, as a standalone antiviral oral intervention candidate for COVID-19

Med, Год журнала: 2024, Номер 5(1), С. 42 - 61.e23

Опубликована: Янв. 1, 2024

BackgroundOral antiviral drugs with improved potency and safety are needed to address current challenges in clinical practice for treatment of COVID-19, including the risks rebound, drug-drug interactions, emerging resistance.MethodsOlgotrelvir (STI-1558) is designed as a next-generation targeting SARS-CoV-2 main protease (Mpro), an essential enzyme replication, human cathepsin L (CTSL), key entry into host cells.FindingsOlgotrelvir highly bioavailable oral prodrug that converted plasma its active form, AC1115. The dual mechanism action olgotrelvir AC1115 was confirmed by activity inhibition assays co-crystal structures Mpro CTSL. displayed inhibiting replication all tested variants cell culture systems. Olgotrelvir also inhibited viral cells using Spike-mediated pseudotypes In K18-hACE2 transgenic mouse model SARS-CoV-2-mediated disease, significantly reduced virus load lungs, prevented body weight loss, cytokine release lung pathologies. demonstrated potent against nirmatrelvir-resistant E166 mutants. showed enhanced bioavailability animal models humans significant exposure without ritonavir. phase I studies (ClinicalTrials.gov: NCT05364840 NCT05523739), favorable profile activity.ConclusionsOlgotrelvir inhibitor CTSL high standalone candidate COVID-19.FundingFunded Sorrento Therapeutics.

Язык: Английский

---

The substitutions L50F, E166A and L167F in SARS-CoV-2 3CLpro are selected by a protease inhibitorin vitroand confer resistance to nirmatrelvir

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2022, Номер unknown

Опубликована: Июнь 7, 2022

Abstract The SARS-CoV-2 main protease (3CLpro) has an indispensable role in the viral life cycle and is a therapeutic target for treatment of COVID-19. potential 3CLpro-inhibitors to select drug-resistant variants needs be established. Therefore, was passaged vitro presence increasing concentrations ALG-097161, probe compound designed context 3CLpro drug discovery program. We identified combination amino acid substitutions (L50F E166A L167F) that associated with > 20x increase EC 50 values nirmatrelvir (PF-07321332) PF-00835231. While two single (E166A provide low-level resistance inhibitors biochemical assay, triple mutant results highest levels (6x 72x). All are significant loss enzymatic activity, suggesting reduction fitness. Structural biology analysis indicates different reduce number inhibitor/enzyme interactions while binding substrate maintained. These observations will important interpretation development clinical setting. Importance Paxlovid first oral antiviral approved infection. Antiviral treatments often resistant viruses. In order guide use novel antivirals it essential understand risk characterize changes genes proteins. this work, we describe time pathway allows develop against . characteristics may predictive situation. our work management COVID-19 next generation inhibitors.

Язык: Английский

---

In vitro and in vivo characterization of SARS-CoV-2 resistance to ensitrelvir

Nature Communications, Год журнала: 2023, Номер 14(1)

Опубликована: Июль 15, 2023

Ensitrelvir, an oral antiviral agent that targets a SARS-CoV-2 main protease (3CLpro or Nsp5), is clinically useful against including its omicron variants. Since most subvariants have reduced sensitivity to monoclonal antibody therapies, resistance other antivirals inhibitors such as ensitrelvir major public health concern. Here, repeating passages of in the presence revealed M49L and E166A substitutions Nsp5 are responsible for ensitrelvir. Both vitro virus growth absence The combination allowed largely evade suppressive effect vitro. possessing Nsp5-M49L showed similar pathogenicity wild-type virus, whereas Nsp5-E166A Nsp5-M49L/E166A slightly attenuated. Ensitrelvir treatment hamsters infected with was ineffective; however, nirmatrelvir molnupiravir effective. Therefore, it important closely monitor emergence ensitrelvir-resistant variants guide selection.

Язык: Английский

---